translate_header: Translate column names into standard names

In QCEWAS: Fast and Easy Quality Control of EWAS Results Files

Translate column names into standard names

Description

This function is used to translate non-standard column names into the standard ones used by EWAS_QC and other functions.

Usage

  translate_header(header,
                   standard = c("PROBEID","BETA","SE","P_VAL"),
                   alternative)

Arguments

header	character vector; the header to be translated.
standard	character vector; the names header should be translated into.
alternative	translation table; see below for more information.

Details

The function takes the entries in standard one by one, and checks them against the translation table for alternatives. It will report any missing standard headers, as well as duplicate ones.

Value

translate_header returns an object of class 'list' with 6 components:

header_h	character vector; the translated header. Unknown columns are included under their old names.
missing_h	character vector; the standard column names that were not found. If none, this returns NULL.
unknown_h	character vector; column names that could not be converted to a standard name. Note that these columns are also included in header_h. If none, this returns NULL.
header_N, missing_N, unknown_N	integer; the lengths of the above three vectors

Translation Table

The translation table must meet the following requirements:

• 2 columns, with the default column names (i.e. the ones in the standard argument) in the first column, and the alternatives in the second.

• Multiple alternatives are allowed for a single standard name, but every alternative name must be in a separate row.

• The alternatives must be capitalized.

• No duplicate alternatives are allowed.

• A header line is not required, and will be ignored if present.

Note

The function will automatically capitalize the elements of the header argument (so the alternatives in the translation table must also be capitalized). Also, elements that are not in standard will not be translated, even if they are present in the translation table.

Examples

# For use in this example, the 2 sample files in the
# extdata folder of the QCEWAS library will be copied
# to your current R working directory
## Not run: 
file.copy(from = file.path(system.file("extdata", package = "QCEWAS"),
                           "sample2.txt.gz"),
          to = getwd(), overwrite = FALSE, recursive = FALSE)
file.copy(from = file.path(system.file("extdata", package = "QCEWAS"),
                           "translation_table.txt"),
          to = getwd(), overwrite = FALSE, recursive = FALSE)

sample_ewas <- read.table("sample2.txt.gz", header = TRUE,
                          stringsAsFactors = FALSE, nrow = 10)
colnames(sample_ewas)


translation_table <- read.table("translation_table.txt", header = TRUE,
                                stringsAsFactors = FALSE)
sample_translation <- translate_header(header = colnames(sample_ewas),
                                       alternative = translation_table)
sample_translation                                         

colnames(sample_ewas) <- sample_translation$header_h

colnames(sample_ewas)

## End(Not run)

QCEWAS documentation built on Feb. 16, 2023, 10:30 p.m.